count: 41 list: - accessibility: Open access additionDate: '2024-01-28T18:03:20.705547Z' biotoolsCURIE: biotools:coconat biotoolsID: coconat collectionID: - Bologna Biocomputing Group community: null confidence_flag: tool cost: Free of charge credit: - email: null fundrefid: null gridid: null name: ELIXIR-ITA-BOLOGNA note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Provider url: null - email: castrense.savojardo2@unibo.it fundrefid: null gridid: null name: Castrense Savojardo note: null orcidid: https://orcid.org/0000-0002-7359-0633 rorid: null typeEntity: Person typeRole: - Primary contact - Developer - Maintainer url: null - email: pierluigi.martelli@unibo.it fundrefid: null gridid: null name: Pier Luigi Martelli note: null orcidid: https://orcid.org/0000-0002-0274-5669 rorid: null typeEntity: Person typeRole: - Primary contact url: null description: CoCoNat is a novel deep-learning based method for predicting coiled-coil regions, register annotation and oligomenrization state. CoCoNat adopts a sequence encoding based on two state-of-the-art protein language models and a deep-learning architetcure to perform prediction. documentation: - note: null type: - Command-line options url: https://github.com/BolognaBiocomp/coconat - note: null type: - User manual url: https://coconat.biocomp.unibo.it/help/ download: - note: null type: Source code url: https://github.com/BolognaBiocomp/coconat version: '1.0' editPermission: authors: - ELIXIR-ITA-BOLOGNA - savo type: group elixirCommunity: [] elixirNode: - Italy elixirPlatform: - Tools elixir_badge: 0 function: - cmd: null input: - data: term: Protein sequence uri: http://edamontology.org/data_2976 format: - term: FASTA uri: http://edamontology.org/format_1929 note: null operation: - term: Protein super-secondary structure prediction uri: http://edamontology.org/operation_0268 output: - data: term: Protein report uri: http://edamontology.org/data_0896 format: - term: HTML uri: http://edamontology.org/format_2331 - term: JSON uri: http://edamontology.org/format_3464 - term: TSV uri: http://edamontology.org/format_3475 homepage: https://coconat.biocomp.unibo.it homepage_status: 0 language: - Python lastUpdate: '2024-03-11T16:30:11.896748Z' license: GPL-3.0 link: [] maturity: Mature name: CoCoNat operatingSystem: - Mac - Linux - Windows otherID: [] owner: ELIXIR-ITA-BOLOGNA publication: - doi: 10.1093/bioinformatics/btad495 metadata: abstract: 'Motivation: Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction methods include the precise identification of CCD boundaries, the annotation of the typical heptad repeat pattern along the coiled-coil helices as well as the prediction of the oligomerization state. Results: In this article, we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries, residue-level register annotation, and oligomerization state. Our method encodes sequences with the combination of two state-of-the-art protein language models and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained Hidden Conditional Random Field for CCD identification and refinement. A final neural network predicts the oligomerization state. When tested on a blind test set routinely adopted, CoCoNat obtains a performance superior to the current state-of-the-art both for residue-level and segment-level CCD. CoCoNat significantly outperforms the most recent state-of-the-art methods on register annotation and prediction of oligomerization states.' authors: - name: Madeo G. - name: Savojardo C. - name: Manfredi M. - name: Martelli P.L. - name: Casadio R. citationCount: 1 date: '2023-08-01T00:00:00Z' journal: Bioinformatics title: 'CoCoNat: a novel method based on deep learning for coiled-coil prediction' note: null pmcid: PMC10425188 pmid: '37540220' type: - Primary version: null - doi: 10.21769/BioProtoc.4935 metadata: abstract: 'Coiled-coil domains (CCDs) are structural motifs observed in proteins in all organisms that perform several crucial functions. The computational identification of CCD segments over a protein sequence is of great importance for its functional characterization. This task can essentially be divided into three separate steps: the detection of segment boundaries, the annotation of the heptad repeat pattern along the segment, and the classification of its oligomerization state. Several methods have been proposed over the years addressing one or more of these predictive steps. In this protocol, we illustrate how to make use of CoCoNat, a novel approach based on protein language models, to characterize CCDs. CoCoNat is, at its release (August 2023), the state of the art for CCD detection. The web server allows users to submit input protein sequences and visualize the predicted domains after a few minutes. Optionally, precomputed segments can be provided to the model, which will predict the oligomerization state for each of them. CoCoNat can be easily integrated into biological pipelines by downloading the standalone version, which provides a single executable script to produce the output.' authors: - name: Manfredi M. - name: Savojardo C. - name: Martelli P.L. - name: Casadio R. citationCount: 0 date: '2024-02-20T00:00:00Z' journal: Bio-protocol title: 'CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences' note: null pmcid: PMC10883893 pmid: '38405078' type: - Usage version: null relation: [] toolType: - Web application - Command-line tool topic: - term: Protein structure analysis uri: http://edamontology.org/topic_2814 - term: Protein folds and structural domains uri: http://edamontology.org/topic_0736 validated: 0 version: - '1.0' - accessibility: null additionDate: '2016-04-15T11:52:42Z' biotoolsCURIE: biotools:comparems2 biotoolsID: comparems2 collectionID: - ms-utils - Proteomics community: null confidence_flag: null cost: Free of charge credit: - email: null fundrefid: null gridid: null name: lumc.nl note: null orcidid: null rorid: null typeEntity: Institute typeRole: - Support url: https://www.lumc.nl - email: magnus.palmblad@gmail.com fundrefid: null gridid: null name: Magnus Palmblad note: null orcidid: http://orcid.org/0000-0002-5865-8994 rorid: null typeEntity: Person typeRole: - Developer - Primary contact - Documentor url: https://github.com/magnuspalmblad - email: null fundrefid: null gridid: null name: Rob Marissen note: null orcidid: https://orcid.org/0000-0002-1220-9173 rorid: null typeEntity: Person typeRole: - Developer url: https://github.com/524D description: compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats. documentation: - note: null type: - General - Command-line options url: http://www.ms-utils.org/compareMS2.html - note: null type: - General - User manual - Command-line options - Installation instructions url: https://github.com/524D/compareMS2 download: - note: null type: Source code url: http://www.ms-utils.org/compareMS2.c version: '1.0' - note: null type: Binaries url: http://www.ms-utils.org/compareMS2.html version: '1.0' - note: null type: Source code url: http://www.ms-utils.org/compareMS2.c version: '1.0' - note: null type: Source code url: https://github.com/524D/compareMS2/tree/main/src version: '2.0' - note: null type: Binaries url: https://github.com/524D/compareMS2/tree/main version: '2.0' editPermission: authors: - proteomics.bio.tools type: group elixirCommunity: - Proteomics elixirNode: - Netherlands elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Mass spectrometry data uri: http://edamontology.org/data_2536 format: - term: MGF uri: http://edamontology.org/format_3651 note: null operation: - term: Comparison uri: http://edamontology.org/operation_2424 - term: Phylogenetic tree visualisation uri: http://edamontology.org/operation_0567 output: - data: term: Species tree uri: http://edamontology.org/data_3272 format: - term: PNG uri: http://edamontology.org/format_3603 - term: SVG uri: http://edamontology.org/format_3604 - data: term: Distance matrix uri: http://edamontology.org/data_2855 format: - term: mega uri: http://edamontology.org/format_1991 - term: Nexus format uri: http://edamontology.org/format_1912 - term: newick uri: http://edamontology.org/format_1910 homepage: https://github.com/524D/compareMS2 homepage_status: 0 language: - C - JavaScript lastUpdate: '2024-02-13T15:35:10.776331Z' license: MIT link: - note: null type: - Repository url: https://github.com/524D/compareMS2 - note: null type: - Software catalogue url: https://www.ms-utils.org/compareMS2.html maturity: Mature name: compareMS2 operatingSystem: - Linux - Windows - Mac otherID: [] owner: n.m.palmblad@lumc.nl publication: - doi: 10.1002/rcm.6162 metadata: abstract: 'Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.' authors: - name: Palmblad M. - name: Deelder A.M. citationCount: 28 date: '2012-04-15T00:00:00Z' journal: Rapid Communications in Mass Spectrometry title: Molecular phylogenetics by direct comparison of tandem mass spectra note: null pmcid: null pmid: '22368051' type: - Primary version: '1.0' - doi: 10.1021/acs.jproteome.2c00457 metadata: abstract: It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932. authors: - name: Marissen R. - name: Varunjikar M.S. - name: Laros J.F.J. - name: Rasinger J.D. - name: Neely B.A. - name: Palmblad M. citationCount: 2 date: '2023-02-03T00:00:00Z' journal: Journal of Proteome Research title: 'compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets' note: null pmcid: PMC9903320 pmid: '36173614' type: - Other version: '2.0' - doi: 10.1021/acs.jproteome.1c00528 metadata: abstract: Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a "gem"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993. authors: - name: Neely B.A. - name: Palmblad M. citationCount: 1 date: '2021-10-01T00:00:00Z' journal: Journal of Proteome Research title: 'Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics' note: null pmcid: PMC8491155 pmid: '34523928' type: - Review version: '2.0' relation: [] toolType: - Command-line tool - Desktop application topic: - term: Phylogeny uri: http://edamontology.org/topic_0084 - term: Proteomics uri: http://edamontology.org/topic_0121 - term: Metabolomics uri: http://edamontology.org/topic_3172 - term: Proteomics experiment uri: http://edamontology.org/topic_3520 validated: 1 version: - '1.0' - '2.0' - accessibility: Open access additionDate: '2023-11-17T03:14:31.662275Z' biotoolsCURIE: biotools:Scan biotoolsID: Scan collectionID: - Cancer community: null confidence_flag: null cost: null credit: - email: zhangjunpeng411@gmail.com fundrefid: null gridid: null name: Junpeng Zhang note: null orcidid: https://orcid.org/0000-0001-6127-9701 rorid: null typeEntity: null typeRole: [] url: null description: Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data documentation: - note: null type: - Quick start guide url: https://github.com/zhangjunpeng411/Scan download: - note: null type: Source code url: https://github.com/zhangjunpeng411/Scan version: '1.0' editPermission: authors: [] type: public elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: null input: - data: term: Gene expression matrix uri: http://edamontology.org/data_3112 format: [] note: null operation: - term: Gene regulatory network prediction uri: http://edamontology.org/operation_2437 - term: miRNA expression analysis uri: http://edamontology.org/operation_3792 output: - data: term: Pathway or network uri: http://edamontology.org/data_2600 format: [] homepage: https://github.com/zhangjunpeng411/Scan homepage_status: 0 language: - R - MATLAB lastUpdate: '2023-11-17T07:03:20.353905Z' license: AGPL-3.0 link: - note: null type: - Repository url: https://github.com/zhangjunpeng411/Scan maturity: null name: Scan operatingSystem: - Mac - Linux - Windows otherID: [] owner: zhangjunpeng publication: [] relation: [] toolType: - Script topic: - term: Bioinformatics uri: http://edamontology.org/topic_0091 - term: Gene regulation uri: http://edamontology.org/topic_0204 - term: Molecular interactions, pathways and networks uri: http://edamontology.org/topic_0602 - term: Transcriptomics uri: http://edamontology.org/topic_3308 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2021-11-30T11:10:36.326367Z' biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_protein-ligand_docking biotoolsID: bioexcel_building_blocks_tutorials_protein-ligand_docking collectionID: - BioExcel community: null confidence_flag: null cost: Free of charge credit: - email: null fundrefid: null gridid: null name: BioExcel Center of Excellence for Computational Biomolecular Research note: null orcidid: null rorid: null typeEntity: Consortium typeRole: - Provider url: https://www.bioexcel.eu - email: genis.bayarri@irbbarcelona.org fundrefid: null gridid: null name: Genís Bayarri note: null orcidid: https://orcid.org/0000-0003-0513-0288 rorid: null typeEntity: Person typeRole: - Developer - Documentor - Maintainer url: https://www.irbbarcelona.org/en/research/genis-bayarri - email: adam.hospital@irbbarcelona.org fundrefid: null gridid: null name: Adam Hospital note: null orcidid: https://orcid.org/0000-0002-8291-8071 rorid: null typeEntity: Person typeRole: - Primary contact url: https://www.irbbarcelona.org/en/research/adam-hospital description: This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). documentation: - note: Read the Docs Workflow Documentation (PDB Cluster90 Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.html - note: Read the Docs Workflow Documentation (PDBe REST-API Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.html - note: Read the Docs Workflow Documentation (Fpocket Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.html download: - note: null type: Source code url: https://github.com/bioexcel/biobb_wf_virtual-screening version: '1.0' editPermission: authors: - gelpi@ub.edu type: group elixirCommunity: [] elixirNode: - Spain - UK elixirPlatform: - Interoperability - Tools elixir_badge: 0 function: - cmd: null input: - data: term: Protein structure uri: http://edamontology.org/data_1460 format: - term: PDB uri: http://edamontology.org/format_1476 - data: term: Small molecule structure uri: http://edamontology.org/data_1463 format: - term: PDB uri: http://edamontology.org/format_1476 - term: SDF uri: http://edamontology.org/format_3814 note: null operation: - term: Protein-ligand docking uri: http://edamontology.org/operation_0482 - term: Structure visualisation uri: http://edamontology.org/operation_0570 output: - data: term: Protein-ligand complex uri: http://edamontology.org/data_1461 format: - term: PDB uri: http://edamontology.org/format_1476 homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bs homepage_status: 0 language: - Python lastUpdate: '2023-08-31T07:34:58.172062Z' license: Apache-2.0 link: - note: Tutorial in HTML (PDB Cluster90 Binding Site Version) type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bs - note: Tutorial in Read The Docs (PDB Cluster90 Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.html - note: Source Code in GitHub type: - Repository url: https://github.com/bioexcel/biobb_wf_virtual-screening - note: Tutorial in HTML (PDBe REST-API Binding Site Version) type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_ebi - note: Tutorial in Read the Docs (PDBe REST-API Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.html - note: Tutorial in HTML (Fpocket Binding Site Version) type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_fpocket - note: Tutorial in Read the Docs (Fpocket Binding Site Version) type: - Other url: https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.html maturity: Emerging name: 'BioExcel Building Blocks tutorials: Protein-ligand Docking' operatingSystem: - Mac - Linux - Windows otherID: [] owner: adam.hospital@irbbarcelona.org publication: - doi: 10.1038/s41597-019-0177-4 metadata: abstract: In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. authors: - name: Andrio P. - name: Hospital A. - name: Conejero J. - name: Jorda L. - name: Del Pino M. - name: Codo L. - name: Soiland-Reyes S. - name: Goble C. - name: Lezzi D. - name: Badia R.M. - name: Orozco M. - name: Gelpi J.L. citationCount: 33 date: '2019-12-01T00:00:00Z' journal: Scientific Data title: BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows note: null pmcid: PMC6736963 pmid: '31506435' type: - Other version: null relation: - biotoolsID: biobb type: uses - biotoolsID: autodock_vina type: uses - biotoolsID: fpocket type: uses - biotoolsID: pdbe type: uses toolType: - Workflow topic: - term: Molecular modelling uri: http://edamontology.org/topic_2275 - term: Structure prediction uri: http://edamontology.org/topic_0082 - term: Data visualisation uri: http://edamontology.org/topic_0092 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2023-08-31T07:04:02.274853Z' biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_protein_conformational_transitions biotoolsID: bioexcel_building_blocks_tutorials_protein_conformational_transitions collectionID: - BioExcel community: null confidence_flag: null cost: Free of charge credit: - email: adam.hospital@irbbarcelona.org fundrefid: null gridid: null name: Adam Hospital Gasch note: null orcidid: https://orcid.org/0000-0002-8291-8071 rorid: null typeEntity: Person typeRole: - Primary contact - Developer - Documentor - Maintainer url: https://www.irbbarcelona.org/en/research/adam-hospital - email: genis.bayarri@irbbarcelona.org fundrefid: null gridid: null name: Genís Bayarri note: null orcidid: https://orcid.org/0000-0003-0513-0288 rorid: null typeEntity: Person typeRole: - Contributor - Developer - Maintainer url: https://www.irbbarcelona.org/es/research/genis-bayarri - email: null fundrefid: null gridid: null name: BioExcel CoE note: null orcidid: null rorid: null typeEntity: Consortium typeRole: - Provider url: https://bioexcel.eu/ description: This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb). documentation: - note: Documentation in Read the Docs type: - Other url: https://biobb-wf-godmd.readthedocs.io/en/latest/index.html download: - note: Source Code in GitHub type: Source code url: https://github.com/bioexcel/biobb_wf_godmd version: '1.0' - note: BioExcel Binder type: VM image url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_godmd/main?filepath=biobb_wf_godmd%2Fnotebooks%2Fbiobb_wf_godmd.ipynb version: null editPermission: authors: [] type: private elixirCommunity: [] elixirNode: - Spain - UK elixirPlatform: - Tools - Interoperability elixir_badge: 0 function: - cmd: null input: - data: term: Protein structure uri: http://edamontology.org/data_1460 format: - term: PDB uri: http://edamontology.org/format_1476 note: null operation: - term: Protein modelling uri: http://edamontology.org/operation_0477 - term: Molecular dynamics uri: http://edamontology.org/operation_2476 - term: Structure analysis uri: http://edamontology.org/operation_2480 - term: Structure visualisation uri: http://edamontology.org/operation_0570 - term: Trajectory visualization uri: http://edamontology.org/operation_3890 output: - data: term: Trajectory data uri: http://edamontology.org/data_3870 format: - term: mdcrd uri: http://edamontology.org/format_3878 - term: PCAzip uri: http://edamontology.org/format_3874 homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd homepage_status: 0 language: - Python lastUpdate: '2023-08-31T07:33:54.784700Z' license: Apache-2.0 link: - note: Tutorial in HTML type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd - note: Tutorial in Read the Docs type: - Other url: https://biobb-wf-godmd.readthedocs.io/en/latest/index.html - note: Source Code in GitHub type: - Repository url: https://github.com/bioexcel/biobb_wf_godmd maturity: Emerging name: 'BioExcel Building Blocks tutorials: Protein Conformational Transitions' operatingSystem: - Mac - Linux - Windows otherID: [] owner: adam.hospital@irbbarcelona.org publication: - doi: 10.1038/s41597-019-0177-4 metadata: abstract: In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. authors: - name: Andrio P. - name: Hospital A. - name: Conejero J. - name: Jorda L. - name: Del Pino M. - name: Codo L. - name: Soiland-Reyes S. - name: Goble C. - name: Lezzi D. - name: Badia R.M. - name: Orozco M. - name: Gelpi J.L. citationCount: 33 date: '2019-12-01T00:00:00Z' journal: Scientific Data title: BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows note: BioExcel Building Blocks (BioBB) pmcid: PMC6736963 pmid: '31506435' type: - Other version: null - doi: 10.1093/bioinformatics/btt324 metadata: abstract: 'Motivation: A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, ...) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).Availability: Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.Contact: or modesto@mmb.pcb.ub.esSupplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press.' authors: - name: Sfriso P. - name: Hospital A. - name: Emperador A. - name: Orozco M. citationCount: 24 date: '2013-08-15T00:00:00Z' journal: Bioinformatics title: Exploration of conformational transition pathways from coarse-grained simulations note: GOdMD method pmcid: null pmid: '23740746' type: - Other version: null relation: - biotoolsID: biobb type: uses - biotoolsID: godmd type: uses - biotoolsID: water type: uses toolType: - Workflow topic: - term: Protein structure analysis uri: http://edamontology.org/topic_2814 - term: Biomolecular simulation uri: http://edamontology.org/topic_3892 - term: Protein sites, features and motifs uri: http://edamontology.org/topic_3510 - term: Molecular modelling uri: http://edamontology.org/topic_2275 - term: Protein structure analysis uri: http://edamontology.org/topic_2814 - term: Data visualisation uri: http://edamontology.org/topic_0092 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2023-08-29T13:59:17.320256Z' biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_molecular_interaction_potentials biotoolsID: bioexcel_building_blocks_tutorials_molecular_interaction_potentials collectionID: - BioExcel community: null confidence_flag: null cost: Free of charge credit: - email: adam.hospital@irbbarcelona.org fundrefid: null gridid: null name: Adam Hospital note: null orcidid: https://orcid.org/0000-0002-8291-8071 rorid: null typeEntity: Person typeRole: - Primary contact - Developer - Documentor - Maintainer url: https://www.irbbarcelona.org/en/research/adam-hospital - email: genis.bayarri@irbbarcelona.org fundrefid: null gridid: null name: Genís Bayarri note: null orcidid: https://orcid.org/0000-0003-0513-0288 rorid: null typeEntity: Person typeRole: - Contributor - Developer - Maintainer url: https://www.irbbarcelona.org/es/research/genis-bayarri - email: null fundrefid: null gridid: null name: BioExcel CoE note: null orcidid: null rorid: null typeEntity: Consortium typeRole: - Provider url: https://bioexcel.eu/ description: This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures step by step, using the BioExcel Building Blocks library (biobb) documentation: - note: Read the Docs workflow documentation type: - Other url: https://biobb-wf-cmip.readthedocs.io/en/latest/index.html download: - note: null type: Source code url: https://github.com/bioexcel/biobb_wf_cmip version: '1.0' - note: BioExcel Binder type: VM image url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_cmip/main?filepath=biobb_wf_cmip%2Fnotebooks%2Fbiobb_wf_cmip.ipynb version: null editPermission: authors: [] type: private elixirCommunity: [] elixirNode: - Spain - UK elixirPlatform: - Tools - Interoperability elixir_badge: 0 function: - cmd: null input: - data: term: Protein structure uri: http://edamontology.org/data_1460 format: - term: PDB uri: http://edamontology.org/format_1476 - data: term: Trajectory data uri: http://edamontology.org/data_3870 format: - term: PDB uri: http://edamontology.org/format_1476 note: null operation: - term: Residue interaction calculation uri: http://edamontology.org/operation_0248 - term: Structure analysis uri: http://edamontology.org/operation_2480 - term: Protein-protein interaction analysis uri: http://edamontology.org/operation_2949 - term: Residue contact prediction uri: http://edamontology.org/operation_0272 - term: Structure visualisation uri: http://edamontology.org/operation_0570 output: - data: term: Protein interaction data uri: http://edamontology.org/data_0906 format: - term: Textual format uri: http://edamontology.org/format_2330 - data: term: Protein structure uri: http://edamontology.org/data_1460 format: - term: PDB uri: http://edamontology.org/format_1476 - data: term: Protein features uri: http://edamontology.org/data_1277 format: - term: Textual format uri: http://edamontology.org/format_2330 homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmip homepage_status: 0 language: - Python lastUpdate: '2023-08-31T07:32:33.263623Z' license: Apache-2.0 link: - note: Tutorial in HTML type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmip - note: Tutorial in Read The Docs type: - Other url: https://biobb-wf-cmip.readthedocs.io/en/latest/index.html - note: Source Code in GitHub type: - Repository url: https://github.com/bioexcel/biobb_wf_cmip maturity: Emerging name: 'BioExcel Building Blocks tutorials: Molecular Interaction Potentials' operatingSystem: - Mac - Linux - Windows otherID: [] owner: adam.hospital@irbbarcelona.org publication: - doi: 10.1038/s41597-019-0177-4 metadata: abstract: In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. authors: - name: Andrio P. - name: Hospital A. - name: Conejero J. - name: Jorda L. - name: Del Pino M. - name: Codo L. - name: Soiland-Reyes S. - name: Goble C. - name: Lezzi D. - name: Badia R.M. - name: Orozco M. - name: Gelpi J.L. citationCount: 33 date: '2019-12-01T00:00:00Z' journal: Scientific Data title: BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows note: BioExcel Building Blocks (BioBB) pmcid: PMC6736963 pmid: '31506435' type: - Other version: null relation: - biotoolsID: biobb type: uses - biotoolsID: nglview type: uses - biotoolsID: classical_molecular_interaction_potentials_cmip type: uses toolType: - Workflow topic: - term: Biomolecular simulation uri: http://edamontology.org/topic_3892 - term: Protein interactions uri: http://edamontology.org/topic_0128 - term: Data visualisation uri: http://edamontology.org/topic_0092 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2023-08-29T10:55:17.540852Z' biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibility biotoolsID: bioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibility collectionID: - BioExcel community: null confidence_flag: null cost: Free of charge credit: - email: adam.hospital@irbbarcelona.org fundrefid: null gridid: null name: Adam Hospital note: null orcidid: https://orcid.org/0000-0002-8291-8071 rorid: null typeEntity: Person typeRole: - Primary contact - Developer - Documentor - Maintainer url: https://www.irbbarcelona.org/en/research/adam-hospital - email: genis.bayarri@irbbarcelona.org fundrefid: null gridid: null name: Genís Bayarri note: null orcidid: https://orcid.org/0000-0003-0513-0288 rorid: null typeEntity: Person typeRole: - Contributor - Developer - Maintainer url: https://www.irbbarcelona.org/es/research/genis-bayarri - email: null fundrefid: null gridid: null name: BioExcel CoE note: null orcidid: null rorid: null typeEntity: Consortium typeRole: - Provider url: https://bioexcel.eu/ description: This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures using Coarse-Grained tools from the FlexServ server and analysing its molecular flexibility documentation: - note: Read The Docs workflow documentation type: - Other url: https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html download: - note: null type: Source code url: https://github.com/bioexcel/biobb_wf_flexserv version: '1.0' - note: BioExcel Binder type: VM image url: https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_flexserv/main?filepath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynb version: '1.0' editPermission: authors: [] type: private elixirCommunity: [] elixirNode: - Spain - UK elixirPlatform: - Tools - Interoperability elixir_badge: 0 function: - cmd: null input: - data: term: Protein structure uri: http://edamontology.org/data_1460 format: - term: PDB uri: http://edamontology.org/format_1476 note: null operation: - term: Protein structure prediction uri: http://edamontology.org/operation_0474 - term: Protein structure analysis uri: http://edamontology.org/operation_2406 - term: Essential dynamics uri: http://edamontology.org/operation_3891 - term: Trajectory visualization uri: http://edamontology.org/operation_3890 - term: Protein property calculation uri: http://edamontology.org/operation_0250 - term: Principal component visualisation uri: http://edamontology.org/operation_2939 output: - data: term: Trajectory data uri: http://edamontology.org/data_3870 format: - term: JSON uri: http://edamontology.org/format_3464 - term: PDB uri: http://edamontology.org/format_1476 - term: PCAzip uri: http://edamontology.org/format_3874 homepage: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexserv homepage_status: 0 language: - Python lastUpdate: '2023-08-29T10:55:17.543854Z' license: Apache-2.0 link: - note: Main web site (BioBB Workflows) type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows#macromolecular-coarse-grained-flexibility - note: Tutorial in HTML type: - Other url: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexserv - note: Tutorial in Read The Docs type: - Other url: https://biobb-wf-flexserv.readthedocs.io/en/latest/index.html - note: Source Code in GitHub type: - Repository url: https://github.com/bioexcel/biobb_wf_flexserv maturity: Emerging name: 'BioExcel Building Blocks tutorials: Macromolecular Coarse-Grained Flexibility' operatingSystem: - Mac - Linux - Windows otherID: [] owner: adam.hospital@irbbarcelona.org publication: - doi: 10.1038/s41597-019-0177-4 metadata: abstract: In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. authors: - name: Andrio P. - name: Hospital A. - name: Conejero J. - name: Jorda L. - name: Del Pino M. - name: Codo L. - name: Soiland-Reyes S. - name: Goble C. - name: Lezzi D. - name: Badia R.M. - name: Orozco M. - name: Gelpi J.L. citationCount: 33 date: '2019-12-01T00:00:00Z' journal: Scientific Data title: BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows note: BioExcel Building Blocks (BioBB) pmcid: PMC6736963 pmid: '31506435' type: - Other version: null relation: - biotoolsID: biobb type: uses - biotoolsID: flexserv type: uses - biotoolsID: nglview type: uses - biotoolsID: pcasuite type: uses toolType: - Workflow topic: - term: Biomolecular simulation uri: http://edamontology.org/topic_3892 - term: Structure analysis uri: http://edamontology.org/topic_0081 - term: Sequence sites, features and motifs uri: http://edamontology.org/topic_0160 - term: Structure prediction uri: http://edamontology.org/topic_0082 - term: Data visualisation uri: http://edamontology.org/topic_0092 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2023-08-01T00:26:20.371769Z' biotoolsCURIE: biotools:GERONIMO biotoolsID: GERONIMO collectionID: [] community: null confidence_flag: null cost: Free of charge credit: - email: agata.kilar@gmail.com fundrefid: null gridid: null name: Agata Kilar note: null orcidid: https://orcid.org/0000-0003-3876-6581 rorid: null typeEntity: null typeRole: - Developer url: null description: GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms. documentation: - note: null type: - User manual url: https://github.com/amkilar/GERONIMO.git download: - note: null type: Source code url: https://github.com/amkilar/GERONIMO.git version: '1.0' editPermission: authors: [] type: private elixirCommunity: [] elixirNode: [] elixirPlatform: - Tools elixir_badge: 0 function: [] homepage: https://github.com/amkilar/GERONIMO.git homepage_status: 0 language: - Python - R - Bash lastUpdate: '2023-08-01T00:36:04.641143Z' license: MIT link: [] maturity: Mature name: GERONIMO operatingSystem: - Windows - Linux otherID: [] owner: amkilar publication: [] relation: - biotoolsID: infernal type: uses toolType: - Workflow - Command-line tool topic: - term: Evolutionary biology uri: http://edamontology.org/topic_3299 - term: Sequence analysis uri: http://edamontology.org/topic_0080 - term: Phylogenetics uri: http://edamontology.org/topic_3293 validated: 0 version: - '1.0' - accessibility: Open access additionDate: '2023-07-26T14:34:25.798022Z' biotoolsCURIE: biotools:kojak biotoolsID: kojak collectionID: [] community: null confidence_flag: null cost: Free of charge credit: [] description: A database search algorithm for solving cross-linked peptide mass spectra. documentation: - note: null type: - Quick start guide - Installation instructions - User manual url: https://kojak-ms.systemsbiology.net/docs/index.html - note: null type: - Command-line options url: https://kojak-ms.systemsbiology.net/param/index.html download: - note: null type: Downloads page url: https://kojak-ms.systemsbiology.net/download.html version: 1.0 - 2.0.0 editPermission: authors: [] type: private elixirCommunity: - Proteomics elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: [] homepage: https://kojak-ms.systemsbiology.net/ homepage_status: 0 language: - C++ lastUpdate: '2023-07-26T14:48:27.327393Z' license: Apache-2.0 link: [] maturity: Mature name: Kojak operatingSystem: - Linux - Windows otherID: [] owner: mhoopmann publication: - doi: 10.1021/pr501321h metadata: abstract: Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and freely available. This software provides both existing and new cross-linking researchers alike an effective way to derive additional cross-link identifications from new or existing data sets. For new users, it provides a simple analytical resource resulting in more cross-link identifications than other methods. authors: - name: Hoopmann M.R. - name: Zelter A. - name: Johnson R.S. - name: Riffle M. - name: Maccoss M.J. - name: Davis T.N. - name: Moritz R.L. citationCount: 126 date: '2015-05-01T00:00:00Z' journal: Journal of Proteome Research title: 'Kojak: Efficient analysis of chemically cross-linked protein complexes' note: null pmcid: PMC4428575 pmid: '25812159' type: - Primary version: '1.0' - doi: 10.1021/acs.jproteome.2c00670 metadata: abstract: Fragmentation ion spectral analysis of chemically cross-linked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of cross-links improve the sensitivity and accuracy of correct cross-link identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multiplatform. authors: - name: Hoopmann M.R. - name: Shteynberg D.D. - name: Zelter A. - name: Riffle M. - name: Lyon A.S. - name: Agard D.A. - name: Luan Q. - name: Nolen B.J. - name: MacCoss M.J. - name: Davis T.N. - name: Moritz R.L. citationCount: 0 date: '2023-02-03T00:00:00Z' journal: Journal of Proteome Research title: Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline note: null pmcid: PMC10234491 pmid: '36629399' type: - Primary version: 2.0.0 relation: [] toolType: - Command-line tool topic: - term: Proteomics uri: http://edamontology.org/topic_0121 - term: Proteomics experiment uri: http://edamontology.org/topic_3520 - term: Proteins uri: http://edamontology.org/topic_0078 validated: 0 version: - 2.0.0 - accessibility: Open access additionDate: '2023-07-03T10:51:19.368916Z' biotoolsCURIE: biotools:suchtree biotoolsID: suchtree collectionID: [] community: null confidence_flag: null cost: Free of charge credit: - email: null fundrefid: null gridid: null name: Russell Y. Neches note: null orcidid: https://orcid.org/0000-0002-2055-8381 rorid: null typeEntity: Person typeRole: - Primary contact url: https://vort.org - email: null fundrefid: null gridid: null name: Camille Scott note: null orcidid: https://orcid.org/0000-0001-8822-8779 rorid: null typeEntity: Person typeRole: - Contributor url: http://www.camillescott.org/ description: A Python library for doing fast, thread-safe computations with phylogenetic trees. documentation: - note: null type: - General url: https://github.com/ryneches/SuchTree#readme download: - note: null type: Software package url: https://pypi.org/project/SuchTree/ version: '1.0' editPermission: authors: [] type: private elixirCommunity: [] elixirNode: [] elixirPlatform: [] elixir_badge: 0 function: - cmd: SuchTree.distances_by_name() input: - data: term: Gene tree uri: http://edamontology.org/data_3271 format: - term: newick uri: http://edamontology.org/format_1910 note: null operation: - term: Phylogenetic tree distances calculation uri: http://edamontology.org/operation_0557 - term: Phylogenetic tree topology analysis uri: http://edamontology.org/operation_0551 - term: Phylogenetic tree visualisation uri: http://edamontology.org/operation_0567 output: - data: term: Matrix uri: http://edamontology.org/data_2082 format: - term: NumPy format uri: http://edamontology.org/format_4003 homepage: https://github.com/ryneches/SuchTree homepage_status: 0 language: - Python lastUpdate: '2023-07-03T10:51:39.215013Z' license: BSD-3-Clause link: - note: null type: - Repository url: https://github.com/ryneches/SuchTree - note: null type: - Issue tracker url: https://github.com/ryneches/SuchTree/issues maturity: Emerging name: SuchTree operatingSystem: - Mac - Linux - Windows otherID: [] owner: ryneches publication: - doi: 10.21105/joss.00678 metadata: null note: null pmcid: null pmid: null type: - Primary version: '0.7' relation: [] toolType: - Library topic: - term: Phylogeny uri: http://edamontology.org/topic_0084 validated: 0 version: [] next: ?page=2 previous: null